Tag: general concepts

Parameter/Reference Tagging

Updated: March 28, 2019

Parameter and reference files may be ’tagged’ (i.e. given a nickname). These tags can then be used in place of the file name itself. A tag in cpptraj is recognized by being bounded by brackets (’[’ and ’]’)…. Read More

Category: CPPTRAJ, General Concepts

Tags: analysis, general concepts, mask, running cpptraj

Ranges

Posted: February 20, 2019

Ranges instead of atom masks. For several commands some arguments are ranges (e.g. ’trajout onlyframes <range>’, ’nastruct resrange<range>’, ’rmsd perres range <range>’); THESE ARE NOT ATOM MASKS. They are simple number ranges using ’-’ to specify a range… Read More

Category: CPPTRAJ, General Concepts

Tags: general concepts, mask, ranges

Atom Mask Selection Syntax

Updated: January 26, 2024

The mask syntax is similar to PTRAJ. Note that the characters ’:’, ’@’, and ’*’ are reserved for masks and should not be used in output file or data set names. All masks are case-sensitive. Either names or… Read More

Category: CPPTRAJ, General Concepts

Tags: general concepts, mask

Units

Updated: February 20, 2019

Cpptraj uses the AKMA system of units. The exception is time, which is typically expressed in ps (except where noted). Variable Unit Length Angstrom Energy kcal/mol Mass AMU Charge electron Time ps (typically) Force kcal/mol*Angstrom

Category: CPPTRAJ, General Concepts

Tags: general concepts, units